Ok after reading through the arguments and everyone claiming what the text states i decided to make it clear:
Stone Warden (Ex): Beginning at 2nd level, a deepwarden knows how to use his strengths to compensate for his weaknesses. He adds his Constitution bonus to AC instead of his Dexterity, if the character's Constitution bonus is higher. The deepwarden loses this bonus to his Armor Class whenever he would normally be denied his Dexterity bonus to AC. In such a situation, the deepwarden would still be considered flat-footed.
these courtesy of the wizards web site.
it clearly states
1. his gets con bonus to AC and does not receive his Dex bonus to AC. if, and only if (implied), his con bonus is higher.
2. when he would be denied his dexterity bonus to AC he doesn't gain the benefits of having his con bonus to AC. It explicitly states flat-footed which is the only condition that prevents dex to AC, others such as hold person cause flat-footed and indirectly cause loss of dex to AC.
in the phb it is clearly stated a specific but contradictory rule, such as using con instead of dex to ac, trumps the general rule.
no where in there does it mention max dexterity concerning armors. As such there is no specific rule to trump the limiting of Dex to AC general rule, thus it can not be applied to Con, there is no ambiguity.
Is this what they intended? I don't know, but it is what they wrote. And honestly if you feel that it causes the deepwarden to have too high an AC just house rule it. If the difference of a few points of AC is that big of a deal in your game then the DM is in trouble, there will be far more difficult things to handle that they won't be able to deal with.
edit to change gears:
As to the Rainbow Servant. This is reiterating the fact that text trumps tables. It was a case of the right hand not knowing what the left hand was doing. It is a PrC and a Base class that were from different books and interacted in a way that neither author had considered, because each changed the rules for spell knowledge slightly. Had it been a sorcerer taking the PrC no problem he can only learn so many spells off the cleric list, a wizard is similar in that he has to find scrolls of them and would likely be better suited going into another PrC. Warmage/DreadNecro/Beguiler get much more out of this as they need expanded spell lists to stay competitive but goes overboard with knowing every cleric spell. They are also at an advantage over the cleric in that they aren't limited in their casting of spells that have a descriptor against their alignment.
So to sum up that last paragraph the ruling is correct but the the interaction of rules is flawed and any DM should carefully consider the interaction of said base classes with that PrC.